1 | background
2 | questions
3 | approaches
4 | methods
5 | results
6 | future
Cercocarpus
March 1st, ’23
1 | background
2 | questions
3 | approaches
4 | methods
5 | results
6 | future
Cercocarpus
Jane Ogilvie (ecological fieldwork, design)
Emily J. Woodworth (pollen morphology, and microscopy)
Sophie Taddeo (geo-spatial, statistics)
Paul CaraDonna (little bees/big picture(s))
Jeremie Fant (all things molecular and tied together)
i.e. an in-house production.
FQI calculated from AIM
Cirsium scariosum
Macroinvertebrates.org
Solidago spathulata & Megachile wheeleri, by A. Litz
Five Astragali
Rhododendron sp. Hengduan Mtns., by Qin Li
Do the number of sequence reads reflect the amount of biological material in a sample?
FPNW 2nd 2018
USFWS
workflow
Corbiculae Sample
a single species
tissue from Rocky Mountain Herbarium
hyb-seq
Cirsium scariosum
Reclassification table
Regress the proportion of all identifiable pollen grains in each sample against the total percent sequence reads for those morphotypes
database
| Metric | Value | Metric | Value |
|---|---|---|---|
| Accuracy (Training) | 83.75 | F-Score | 0.84 |
| Accuracy (Test) | 84.00 | AUC | 0.92 |
| Recall | 81.03 | Concordance | 0.92 |
| True Neg. Rate | 86.97 | Discordance | 0.08 |
| Precision | 88.04 | Tied | 0.00 |
| ml | lm | |
|---|---|---|
| ensembles | 493 | 473 |
| true + | 362 | 286 |
| true - | 33 | 55 |
| false + | 64 | 41 |
| false - | 34 | 93 |
flower dates
flower dates
ca. 80% of samples made it through to analysis
Species in Sequence DB
Three Initial Networks
| Condition | No. Class. | Prcnt. Class. | Total Seqs | Rank |
|---|---|---|---|---|
| A | 143 | 21.0 | 32.0 | Species |
| B | 205 | 30.1 | 10.5 | Species |
| C | 5 | 0.7 | 0.4 | Genus |
| G | 29 | 4.3 | 7.8 | Species |
| H | 280 | 41.2 | 47.9 | Genus |
| None met | 18 | 2.6 | 1.4 | Multiple |
Counted grains
Some foraging preferences of Bombus, both at this field site and across a great many localities globally emerge from this work, which reiterates the needs for land managers to maintain relatively high amounts of members of the Fabaceae, Boraginaceae, and Ranunculaceae, in Western North American montane landscapes (@goulson2005causes, @goulson2010bumblebees, @liang2021evolutionary, @bontvsutvsnaja2021bumble). Numerous historic, and some ongoing, land management practices reduce the ability of many landscapes to support stable populations of Bombus. Historic livestock grazing was often associated with the targeted removal of many species of plants which are known to have compounds toxic to cattle. In particular, the removal of locoweeds (Fabaceae: Astragalus L. & Oxytropis DC.) and larkspurs (Ranunculaceae: Delphinium) were common across public lands administered by the United States Forest Service (@ralphs1988herbicide, @aldous1919eradicating, @ralphs2003mechanism). Further actions, generally initiated by early settlers, involved the channelization and incising of streams, culling of beavers, and leaving cattle concentrated on higher order stream banks for significant periods of time, all processes which lower the water tables and reduced the extent of stream-associated [riverine] wetlands and the mesic meadows fringes which provide habitat for many species of tall Mertensia (Boraginaceae, e.g. M. ciliata Torr. G. Don.) widely distributed across Western North America, and to an extent Delphinium barbeyi and many species of native Trifolium L. (@dahl1990wetlands, @naiman1988alteration, @belsky1999survey, @cooke1976arroyos). Fire suppression further resulted in the succession of many Aspen (Populus tremuloides Michx.) groves to Conifer stands, decreasing the mosaic of age structured habitats in many landscapes, adversely effects habitat for tall Mertensia species and several species of Delphinium (@brewen202176, @keane2002cascading). Finally the effects of Nitrogen deposition, especially given the West’s rapidly growing population still pose adverse effects on the abundance of a variety of species of Fabaceae at Urban-Rural interfaces (see @stevens2018atmospheric, @fenn2003ecological). Current solutions to these issues, involve targeted burns, reintroduction of beavers and beaver habitat analogs, and the possibility of re-seeding a variety of ‘locoweeds’ and ‘larkspurs’ in areas now seldom used, or only used for early, grazing. The highly enthusiastic response of land managers, and homeowners, to plant Ascelpias L., using genetically appropriate materials, to improve Monarch Butterfly (Danaus plexippus L.) habitat provides an effective framework for the latter (@oberhauser2015monarchs, @basey2015producing).
seem pretty cool and useful, you should use them.
promising
Employment: Yingying Xie (NU), Josh Scholl (NU), Ken Holsinger (BLM), Cassandra Owen (SCC), Sam Isham (UM), Kelly McMillen (UM), Kay Hajek (UM), Linda Vance (UM)
Project: Nyree Zerega, Pat Herendeen, Hilary Noble, Zoe Diaz-Martinez, Angela McDonnell, Elena Loke, Ian Breckheimer, Ben Legler, Ernie Nelson, Charles (Rick) Williams, D. Knoke, L. Brummer, J. Boyd, C. Davidson, I. Gilman, M. Kirkpatrick, S. McCauley, J. Smith, K. Taylor, & C. Williams. David Giblin, Mare Nazaire, Sarah Burnett, Lauren Price, T.C.H. Cole, Eliot Gardner.
Personal: Dad, Mom, Amelia Litz, Melissa, Amanda, Jack, Sim, Mark, Judy & Julia, Jim & Jenny, Matt, Diane, Jim, Jimmy.
github/sagesteppe